Variant report

Variant	rs1573363
Chromosome Location	chr18:45455084-45455085
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:45370062..45371817-chr18:45453252..45455227,2	MCF-7	breast:
2	chr18:45445551..45451271-chr18:45453158..45456977,7	K562	blood:
3	chr18:45412211..45417305-chr18:45454331..45458060,5	MCF-7	breast:
4	chr18:45412744..45415150-chr18:45452720..45455335,2	MCF-7	breast:
5	chr18:45450692..45455196-chr18:45455930..45459309,6	MCF-7	breast:
6	chr18:45439039..45441634-chr18:45452955..45455422,2	MCF-7	breast:
7	chr18:45452201..45455106-chr18:45476820..45479374,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175387	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10432199	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10502890	0.85[CEU][hapmap]
rs10853560	1.00[CEU][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11082638	1.00[CEU][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11082639	0.90[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11082641	0.86[CEU][hapmap]
rs11874858	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12457664	0.85[CEU][hapmap]
rs12458238	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs12604337	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12605333	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12956483	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12968107	1.00[CEU][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12968493	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs12969725	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs1539871	0.91[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1539872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573362	0.83[CEU][hapmap]
rs1613672	0.96[CEU][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1631576	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17741998	1.00[CEU][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1787176	0.96[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1787185	0.93[CEU][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap]
rs1787186	0.92[CEU][hapmap]
rs1787193	0.96[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1787194	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1787195	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1787196	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1787197	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1787198	0.82[EUR][1000 genomes]
rs1792653	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1792655	0.96[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1792667	0.82[EUR][1000 genomes]
rs1792668	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs1792669	1.00[CEU][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1792670	1.00[CEU][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1792671	0.96[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs1792672	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1792674	0.92[CEU][hapmap]
rs1792675	0.96[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1792679	0.93[CEU][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap]
rs1792681	0.88[CEU][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap]
rs1792682	0.93[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs1792683	0.89[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1792686	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs1792687	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1981	0.92[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2000708	0.86[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2000709	0.82[CEU][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2012555	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2096932	0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2096933	0.86[CEU][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28548478	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35710478	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3813068	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4939672	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4940102	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs4940109	0.89[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4940110	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4940120	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4940127	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61513611	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62086544	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6507790	0.93[CEU][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6507791	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs7228393	0.92[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7231538	1.00[CEU][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7232764	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7232893	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7233129	1.00[CEU][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7236177	1.00[CEU][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7237544	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7243502	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs729112	1.00[CEU][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs747952	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs747953	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs765213	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8084915	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8095519	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8097580	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8097912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8097925	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8099127	1.00[CEU][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8099681	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs948600	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs948601	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs948602	0.96[CEU][hapmap]
rs948603	1.00[CEU][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs948604	0.89[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9946556	0.96[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9947494	0.81[EUR][1000 genomes]
rs9950207	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9955626	1.00[CEU][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9961652	0.82[ASN][1000 genomes]
rs9966637	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9966964	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909614	chr18:45419421-45478490	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv909615	chr18:45452321-45493026	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1573363	SMAD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45433200-45455400	Weak transcription	Fetal Brain Male	brain
2	chr18:45435600-45455800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr18:45439000-45456200	Weak transcription	Esophagus	oesophagus
4	chr18:45439000-45456200	Weak transcription	Spleen	Spleen
5	chr18:45439600-45455400	Weak transcription	Fetal Muscle Leg	muscle
6	chr18:45439800-45456200	Weak transcription	Pancreas	Pancrea
7	chr18:45443000-45456000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr18:45444800-45456000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr18:45444800-45456000	Weak transcription	Lung	lung
10	chr18:45446000-45455400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr18:45446200-45455800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr18:45447600-45456000	Weak transcription	Left Ventricle	heart
13	chr18:45450000-45456200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr18:45450200-45455200	Weak transcription	Right Ventricle	heart
15	chr18:45451000-45455600	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr18:45451000-45455600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr18:45451600-45455200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr18:45451600-45456000	Enhancers	Fetal Heart	heart
19	chr18:45452000-45456000	Enhancers	Brain Hippocampus Middle	brain
20	chr18:45452200-45456000	Enhancers	Brain Substantia Nigra	brain
21	chr18:45452400-45455200	Enhancers	Small Intestine	intestine
22	chr18:45452400-45455800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr18:45452400-45455800	Enhancers	Brain Anterior Caudate	brain
24	chr18:45452400-45455800	Enhancers	Fetal Intestine Small	intestine
25	chr18:45452400-45456000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr18:45452600-45456000	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr18:45452800-45456000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr18:45453000-45455800	Enhancers	Brain Angular Gyrus	brain
29	chr18:45453400-45455800	Weak transcription	Aorta	Aorta
30	chr18:45453400-45455800	Enhancers	Liver	Liver
31	chr18:45453600-45456000	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr18:45453600-45458200	Active TSS	GM12878-XiMat	blood
33	chr18:45453800-45455200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr18:45453800-45455800	Weak transcription	Psoas Muscle	Psoas
35	chr18:45453800-45456200	Weak transcription	Gastric	stomach
36	chr18:45454000-45456000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr18:45454000-45456000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr18:45454200-45455200	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr18:45454400-45455200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr18:45454400-45455200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr18:45454400-45455200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr18:45454400-45455600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr18:45454400-45455800	Enhancers	Primary B cells from cord blood	blood
44	chr18:45454400-45455800	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr18:45454400-45456000	Enhancers	Brain Cingulate Gyrus	brain
46	chr18:45454400-45456200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr18:45454400-45456400	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr18:45454400-45456400	Flanking Active TSS	Dnd41	blood
49	chr18:45454600-45455200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr18:45454600-45455200	Flanking Active TSS	Colon Smooth Muscle	Colon

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